You are kind of right.
In a bolt gun with factory ammo, you will never see the difference.
In an AR, if you load to max for a 5.56 chamber you will need to back off about a grain in a true .223 chamber, or you will be picking primers out of your trigger group.
So if we're only talking about < 5% difference in maximum charge with a 5.56 versus .223 chamber ... It seems to me that you easily could find that much difference in any two rifles with the same NOMINAL chambering, correct?